Metabolism and Thermodynamics

Overview of Metabolism

Metabolism refers to all chemical reactions that occur within an organism to maintain life. These reactions transform energy and matter, enabling growth, reproduction, and cellular maintenance.

• Catabolic Pathways: Break down complex molecules into simpler ones, releasing energy (e.g., cellular respiration).

• Anabolic Pathways: Build complex molecules from simpler ones, requiring energy input (e.g., protein synthesis).

Forms of Energy

• Kinetic Energy: Energy of motion; for example, the movement of molecules.

• Potential Energy: Stored energy due to position or structure; for example, energy stored in chemical bonds.

Laws of Thermodynamics

• First Law: Energy cannot be created or destroyed, only transformed ().

• Second Law: Every energy transfer increases the entropy (disorder) of the universe.

• Total Laws: There are two main laws relevant to biology.

Spontaneity and Free Energy

• Spontaneous Reaction: Occurs without energy input; determined by free energy change ().

• Gibbs Free Energy Equation:

• : Change in free energy

• : Change in enthalpy (heat content)

• : Temperature in Kelvin

• : Change in entropy

Exergonic vs. Endergonic Reactions

• Exergonic: Releases energy; ; spontaneous.

• Endergonic: Requires energy input; ; non-spontaneous.

ATP and Coupled Reactions

• ATP: Adenosine triphosphate; main energy currency of the cell.

• Role of ATP: Powers cellular work by transferring a phosphate group to other molecules (phosphorylation).

• Coupled Reactions: Energy released from exergonic reactions is used to drive endergonic reactions.

Enzymes and Metabolic Regulation

• Enzymes: Biological catalysts that speed up metabolic reactions by lowering activation energy.

• Enzyme Specificity: Determined by the shape of the active site; only specific substrates fit.

• Induced Fit Model: Enzyme changes shape slightly to fit substrate more tightly.

• Enzyme Inhibitors: Molecules that decrease enzyme activity (competitive or noncompetitive).

• Regulation: Enzyme activity is regulated to control metabolic pathways and maintain homeostasis.

Activation Energy Diagrams

Diagrams typically show the energy required for a reaction with and without an enzyme. The enzyme lowers the activation energy barrier, making the reaction proceed faster.

Cellular Respiration

Redox Reactions

• Oxidation: Loss of electrons.

• Reduction: Gain of electrons.

• Redox Reaction: Transfer of electrons between molecules, crucial for energy exchange in cells.

Substrate-Level vs. Oxidative Phosphorylation

• Substrate-Level Phosphorylation: Direct transfer of phosphate to ADP from a substrate.

• Oxidative Phosphorylation: ATP synthesis powered by electron transport chain and chemiosmosis.

Stages of Cellular Respiration

• Glycolysis: Occurs in cytoplasm; breaks glucose into pyruvate; produces ATP and NADH.

• Oxidation of Pyruvate: Pyruvate converted to Acetyl CoA in mitochondria.

• Citric Acid Cycle (Krebs Cycle): Occurs in mitochondrial matrix; Acetyl CoA oxidized; produces NADH, FADH2, ATP, CO2.

• Oxidative Phosphorylation: Electron transport chain creates H+ gradient; ATP produced by chemiosmosis.

Inputs and Outputs Table

Electron Transport Chain and Chemiosmosis

• Electron Transport Chain: Series of proteins in the inner mitochondrial membrane; electrons from NADH and FADH2 pass through, pumping H+ ions to create a gradient.

• Chemiosmosis: H+ ions flow back through ATP synthase, driving ATP production.

• Coupling: Exergonic electron flow powers endergonic ATP synthesis.

Fermentation vs. Cellular Respiration

Cell Division and the Cell Cycle

Purpose and Phases of Cell Division

Cell division enables growth, repair, and reproduction. The cell cycle consists of interphase (G1, S, G2), mitosis, and cytokinesis.

• Mitosis: Division of the nucleus to produce two identical daughter cells.

• Products of Mitosis: Two genetically identical diploid cells.

• Exceptions: Mutations or errors can lead to non-identical cells.

DNA Organization

• Genome: Entirety of a cell's DNA.

• Chromosomes: DNA packed into structures; each consists of two sister chromatids joined at a centromere.

Somatic Cells vs. Gametes

• Somatic Cells: Body cells; diploid (2n).

• Gametes: Sex cells; haploid (n).

Phases of the Cell Cycle

• G1 Phase: Cell growth.

• S Phase: DNA replication.

• G2 Phase: Preparation for mitosis.

Steps of Mitosis

• Prophase: Chromosomes condense, spindle forms.

• Metaphase: Chromosomes align at cell equator.

• Anaphase: Sister chromatids separate to opposite poles.

• Telophase: Nuclear envelope reforms, chromosomes decondense.

Mitotic Spindle

• Definition: Structure made of microtubules that segregates chromosomes.

• Attachment: Spindle fibers attach to centromeres via kinetochores.

• Function: Ensures accurate chromosome separation.

Cytokinesis

• Animal Cells: Cleavage furrow forms.

• Plant Cells: Cell plate forms.

Regulation of the Cell Cycle

• Checkpoints: Control progression; prevent uncontrolled division (cancer).

• Regulatory Proteins: Cyclins and cyclin-dependent kinases (CDKs).

Comparison of Cell Cycle Phases

Photosynthesis and Related Processes

Chloroplast Structure

• Outer Membrane: Protective layer.

• Inner Membrane: Regulates passage of materials.

• Stroma: Fluid-filled space; site of Calvin cycle.

• Thylakoid System: Membranous sacs; site of light-dependent reactions.

• Grana: Stacks of thylakoids.

• Thylakoid Lumen: Internal space of thylakoid.

Autotrophs vs. Heterotrophs

• Autotrophs: Produce their own food via photosynthesis (e.g., plants).

• Heterotrophs: Obtain food by consuming other organisms.

NADP+/NADPH Function

• NADP+: Electron carrier; accepts electrons during light reactions.

• NADPH: Reduced form; donates electrons in Calvin cycle.

Photosystems and Photolysis

• Photosystem: Protein complex that absorbs light and transfers electrons.

• Photolysis: Splitting of water to provide electrons; produces O2.

Photosynthesis

• Purpose: Convert solar energy into chemical energy (glucose).

• Stages: Light-dependent reactions (thylakoid), Calvin cycle (stroma).

• Equation:

• Products: Glucose, O2

• Reactants: CO2, H2O, light

Aerobic Respiration

• Purpose: Break down glucose to produce ATP.

• Products: CO2, H2O, ATP

• Location: Mitochondria

Calvin Cycle

• Purpose: Fix carbon to produce glucose.

• Reactants: CO2, ATP, NADPH

• Products: Glucose, ADP, NADP+

• Location: Stroma of chloroplast

Comparison Table: Photosynthesis vs. Aerobic Respiration